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- PDB-7ovg: The C146A variant of an amidase from Pyrococcus horikoshii with b... -

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Basic information

Entry
Database: PDB / ID: 7ovg
TitleThe C146A variant of an amidase from Pyrococcus horikoshii with bound acetamide
ComponentsCN hydrolase domain-containing protein
KeywordsHYDROLASE / Amidase / Nitrilase superfamily
Function / homology
Function and homology information


N-carbamoylputrescine amidase activity / beta-alanine biosynthetic process via 3-ureidopropionate / putrescine biosynthetic process from arginine / beta-ureidopropionase activity
Similarity search - Function
Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
ACETAMIDE / CN hydrolase domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSu, S. / Makumire, S. / Sewell, B.T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Global Challenges Research FundST/R002754/1 United Kingdom
CitationJournal: J.Struct.Biol. / Year: 2022
Title: The structures of the C146A variant of the amidase from Pyrococcus horikoshii bound to glutaramide and acetamide suggest the basis of amide recognition.
Authors: Makumire, S. / Su, S. / Weber, B.W. / Woodward, J.D. / Wangari Kimani, S. / Hunter, R. / Sewell, B.T.
History
DepositionJun 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CN hydrolase domain-containing protein
B: CN hydrolase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0906
Polymers59,9012
Non-polymers1894
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The asymmetric unit contains one complete assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-40 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.979, 57.012, 61.358
Angle α, β, γ (deg.)68.09, 85.16, 76.93
Int Tables number1
Space group name H-MP1

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Components

#1: Protein CN hydrolase domain-containing protein


Mass: 29950.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH0642 / Production host: Escherichia coli (E. coli) / References: UniProt: O58376
#2: Chemical ChemComp-ACM / ACETAMIDE


Mass: 59.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The crystallization condition is: 5mg/mL protein, 0.1M potassium chloride, 0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate ...Details: The crystallization condition is: 5mg/mL protein, 0.1M potassium chloride, 0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.1M acetamide; Imidazole; MES monohydrate (acid); 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 170 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.65→43.86 Å / Num. obs: 53852 / % possible obs: 81.14 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.57 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.035 / Rrim(I) all: 0.065 / Net I/σ(I): 11.32
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 3 % / Rmerge(I) obs: 0.3671 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 2008 / CC1/2: 0.927 / CC star: 0.981 / Rpim(I) all: 0.2463 / Rrim(I) all: 0.4444 / % possible all: 30.28

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YPA

6ypa


Resolution: 1.65→43.85 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.56 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18204 2661 4.9 %RANDOM
Rwork0.15115 ---
obs0.1527 51146 81.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.106 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20.01 Å2
2---0 Å2-0.01 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.65→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4224 0 10 207 4441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0174342
X-RAY DIFFRACTIONr_bond_other_d0.0010.0194220
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.8875856
X-RAY DIFFRACTIONr_angle_other_deg1.1882.6899716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5065530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41121.849238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4915784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6341532
X-RAY DIFFRACTIONr_chiral_restr0.110.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021011
X-RAY DIFFRACTIONr_mcbond_it3.2222.4712114
X-RAY DIFFRACTIONr_mcbond_other3.2072.4672113
X-RAY DIFFRACTIONr_mcangle_it4.133.6842645
X-RAY DIFFRACTIONr_mcangle_other4.1423.6862644
X-RAY DIFFRACTIONr_scbond_it6.613.1842228
X-RAY DIFFRACTIONr_scbond_other6.6083.1842229
X-RAY DIFFRACTIONr_scangle_other9.2084.493211
X-RAY DIFFRACTIONr_long_range_B_refined9.86229.5834668
X-RAY DIFFRACTIONr_long_range_B_other9.87929.4524643
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 89 -
Rwork0.378 1340 -
obs--29.11 %

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